PRMT3

protein-coding

protein arginine methyltransferase 3, the group of 7BS protein arginine methyltranferases

Gene summary

This gene belongs to the protein arginine methyltransferase (PRMT) family. The encoded enzyme catalyzes the methylation of guanidino nitrogens of arginyl residues of proteins. The enzyme acts on 40S ribosomal protein S2 (rpS2), which is its major in-vivo substrate, and is involved in the proper maturation of the 80S ribosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Previous symbols:

HRMT1L3

MANE transcript

NM_005788.4

Inheritance

—

ClinVar variants

U:68B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr11:20,387,558-20,509,338

External References & Databases

Ensembl (ENSG00000185238)

Transcript & Mutation Effects

hg38 • Region Span ~121.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRMT3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005788.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar			4
missense			62 clinvar	1 clinvar	1 clinvar	64
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	68	1	1	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005788.4	RefSeq	NP_005779.1	16	MANE Select
ENST00000331079.11	Ensembl	ENSP00000331879.6	16	MANE Select
NM_001145166.2	RefSeq	NP_001138638.1	14	Standard
NM_001145167.2	RefSeq	NP_001138639.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Histidine Metabolism
Histidinemia
Post-translational protein modification
Metabolism of proteins
RMTs methylate histone arginines

Biological Process

regulation of transcription, DNA-templated
protein methylation
peptidyl-arginine methylation, to asymmetrical-dimethyl arginine
negative regulation of protein ubiquitination
histone arginine methylation

Molecular Function

nucleic acid binding
protein binding
methyltransferase activity
histone-arginine N-methyltransferase activity
protein-arginine N-methyltransferase activity

Cellular Component

nucleus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000331079
Coding exons: 16
Length: 121765
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0999	279	284	0.983	0.0000140	3507
Missense (PolyPhen)		54	75.71	0.71325		993
Synonymous	0.879	91	102	0.889	0.00000540	956
Loss of Function	-0.625	35	31.2	1.12	0.00000151	400

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00070	0.00068	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.00050	0.00049	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Methylates (mono and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in some proteins.;

Recessive Scores

pRec: 0.159

Intolerance Scores

RVIS EVS: -0.38
RVIS percentile EVS: 28.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.999

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium